February 2012 - galaxy-user - lists.galaxyproject.org

ftp Server unavailable
by Florian Peschke 20 Feb '12

20 Feb '12

Greetings, yesterday I used the ftp server to upload my FASTQ files. Today I tried to do this again but I cannot get a connection to the ftp server. Is the server down at the moment or is it another problem due to my account? Thank you for your help Florian

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Error on custom builds on public galaxy server
by Pengfei Yu 17 Feb '12

17 Feb '12

Dear sir or madam, I am using galaxy public server and I am trying to build a custom genome using the function "custom Builds" in "user" section. I specified the Name, Key and uploaded the genome fasta file also the chromosome length file. But when I click "submit", galaxy gave an error information like that: "" *Server Error:* An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) "" I don't know where to find the error logs and how to turn debug on. Could you tell me how to fix the problem and upload the custom builds? Thanks a lot! Pengfei -- Pengfei Yu Center of Biophysics and Computational Biology University of Illinois Urbana-Champaign Illinois, 61820, US Cell phone: 217-898-6301

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Recover lost history from Local instance of Galaxy
by Jane Dorweiler 17 Feb '12

17 Feb '12

Greetings, I am running galaxy locally (I believe it is distribution b258de1e6cea -- downloaded 6 Jan 2012 and haven't upgraded yet), and inadvertantly chose 'create new' under options which 'cleared' the history that I had been working with. I have not run anything since, so nothing should be overwritten, and in fact I can find the COMPLETE list of data files in galaxy-dist/database/files/000. Is there any way that I can recover my history, or can I at least load desired .dat files from within that folder by navigating there using upload data? Any help/recommendations would be greatly appreciated. And yes, I also need to reconfigure my local instance such that it will actually let me SAVE my histories, as it currently tells me I need to be 'logged in', but then won't let me log in. Perhaps there's a fix for that in more recent releases? But one problem at a time. Thank you, Jane -- Jane E. Dorweiler, PhD

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Re: [galaxy-user] Using galaxy for Bacterial RNA-seq
by Jeremy Goecks 17 Feb '12

17 Feb '12

Bomba, I'm not familiar enough with bacterial/prokaryotic transcriptomes to suggest a possible workflow. You might try the standard Tophat-Cufflinks-Cuffcompare/merge-Cuffdiff workflow and see whether you get meaningful results; Tophat runs Bowtie internally, so there's no reason to run Bowtie separately unless there are Bowtie-specific parameters that you need to modify. I've had very little experience with PALMapper and can't speak to its efficacy, either for eukaryotic or prokaryotic transcriptome analyses. Finally, I've cc'd the galaxy-user mailing list. Using this list is the best way to reach the Galaxy user community and get in touch with someone that has used Galaxy to analyze bacterial transcriptomes. Good luck, J. On Feb 16, 2012, at 9:17 AM, Bomba Dam wrote: > Dear Dr. Goecks, > > I am working as a post-doctoral fellow in MPI Marburg, Germany. We am trying to understand the differential expression of genes in a methanotrophic bacterium under different growth conditions. We are sequencing the transcriptome using Illumina Hiseq. As I dont have expertise in programming languages, I found the Galaxy interface very user-friendly for doing such transcriptome analysis. However, I could not find a step wise protocol\workflow for mapping bacterial RNA-seq against the reference genome (we have the completely sequenced genome of our model organism). I have found a detailed step by step workflow for RNA-seq analysis from the University of Alabama web-site (uab.edu) However, it refers to the eukaryotic system. > Most examples provided and used for analysis are from eukaryotic systems. I am a bit confused weather the same workflow will also work well for bacterial systems as there are no splicing events or I should make some modifications. Can you kindly suggest me which workflow should I follow for mapping the bacterial reads (Bowtie, Tophat or PALMapper) and subsequent quantification steps. I want some guidance in this regard. > > With kind regards, > > Bomba Dam > -- > Dr. BOMBA DAM > Alexander von Humboldt Postdoctoral Research Fellow > Max-Planck-Institut für terrestrische Mikrobiologie > Karl-von-Frisch-Straße 10 > D-35043 Marburg, Germany > E mail: bomba.dam(a)mpi-marburg.mpg.de > PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) > > Assistant Professor of Microbiology > Department of Botany, Institute of Science > Visva-Bharati (A Central University) > Santiniketan, West Bengal 731235, India. > E mail: bumba_micro(a)visva-bhatari.ac.in, bumba_micro(a)rediffmail.com; > > > > >

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Megablast question
by Scott Tighe 16 Feb '12

16 Feb '12

Hi all When using Galaxy megablast, is there a simple way to reduce my FASTA files from 23 million reads to 1/2 that size and submit to megablast separately? Thanks -- Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999-6666

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Re: [galaxy-user] duplicate reads
by Jennifer Jackson 16 Feb '12

16 Feb '12

Hello Bao, Trimming is a different operation than removing sequences and could be applied to both RNA and DNA data. Unfortunately, there are no generalized rules that could be applied to all cases. The type of data and the mapping tool will determine if trimming is needed and when it should be done. Some mappers have quality trimming options in the tool form itself (for example, Bowtie, in the full parameter list). These screencasts may help, as would the target mapping tool documentation. http://wiki.g2.bx.psu.edu/Learn/Screencasts see: Basic FASTQ Manipulation Advanced FASTQ Manipulation For next time, please continue to send questions with the "to" address as the mailing list and replies as "reply-all, it helps us greatly with tracking. If anyone else on the mailing list has more help to offer, they are welcome to jump in on the discussion. Although, you would likely need to post to the mailing list the source/format of your query data and which tool you are considering using in order to receive specific advice. Best, Jen Galaxy team On 2/16/12 8:20 AM, vang0280(a)umn.edu wrote: > Dear Jennifer, > > That was very helpful! > > Would this also apply to trimming reads that have a low median or bottom > quartile score as well for RNA Seq data? Would you recommend for Tophat > vs Bowtie vs BWA? > > If not when would you trim reads when wouldn't you trim your reads? > > Thanks > > Bao > > On Feb 15 2012, Jennifer Jackson wrote: > >> Hello Bao, >> >> For RNA-seq analysis, removing any reads would be problematic since >> this would interfere with expression/abundance calculations. For >> mapping, TopHat is the preferred alignment tool for spliced RNA data. >> BWA and Bowtie are tools better suited for DNA mapping. >> >> For Prokaryote genomes, the choice of which alignment tool to use may >> be more flexible (splicing would not be an issue), but understanding >> the parameters for the tool options and how to tune appropriately >> (e.g. for a circular genome) would be important to research and test out. >> >> For more details about TopHat, please see the author's web site >> (including an FAQ) at: http://tophat.cbcb.umd.edu/. A help email is >> also available: tophat.cufflinks(a)gmail.com. >> >> Best, >> >> Jen >> Galaxy team >> >> On 2/15/12 9:39 AM, vang0280(a)umn.edu wrote: >>> Dear all, >>> > When is it necessary to remove duplicate reads from your RNA Seq analysis? >>> Is it required for Tophat versus BWA versus Bowtie? >>> >>> Thanks, >>> Bao >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> at usegalaxy.org. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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FTP in local galaxy Instance
by Paula R. Kuser-Falcao 16 Feb '12

16 Feb '12

Hi, We have set up a local galaxy instance and the settings in the universe file to be able to upload FTPed files. The settings in the universe_wsgi.ini seem correct and are : > > > # This should point to a directory containing subdirectories matching > users' > # email addresses, where Galaxy will look for files. > ftp_upload_dir = /var/www/galaxy-dist/ftp > I have also set ftp_upload_site. But when the users sign into galaxy they cannot view their file in the get data -> from files on my computer. When I use the Galaxy server at main.g2.bx.psu.edu I see the ftp files option no problems. Can you suggest something else I should be doing to have this feature to work? Thanks, Paula Kuser-Falcao

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Problem launching Cloudman console
by Arjun Vadapalli 16 Feb '12

16 Feb '12

When I start the EC2 instance using the public image of 861460482541/galaxy-cloudman-2010-03-22, I do not see the EC2 cluster configuration dialog. I followed all the instructions listed under http://wiki.g2.bx.psu.edu/Admin/Cloud. What I get directly is a cloudman console page which has 0 bytes allocated and inoperative buttons. As per the description in the help page, the Access Galaxy button is supposed to be greyed out but as can be seen in the screen capture I have attached the button is not greyed out. When I click on it the message says that a Cloudman instance is not running. I have attached a screenshot of console page. I am using Internet Explorer as my web browser. I would appreciate any help in understanding what I am doing wrong. Thanks Arjun

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duplicate reads
by vang0280＠umn.edu 16 Feb '12

16 Feb '12

Dear all, When is it necessary to remove duplicate reads from your RNA Seq analysis? Is it required for Tophat versus BWA versus Bowtie? Thanks, Bao

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While executing tool galaxy giving this error
by La Chi 15 Feb '12

15 Feb '12

hi, will you please help me how can i fix this error' thanks Traceback (most recent call last): File "/galaxy-dist/tools/ova/getsitesnotoverlap_tf.py", line 60, in ? if __name__ == "__main__": __main__() File "/galaxy-dist/tools/ova/getsitesnotoverlap_tf.py", line 50, in __main__ result_set = connection.execute( "select * from getsitesnotoverlap_tf (" + userid + "," + tfid + "," + bpover + "," + ch + "," + sf +")" ) File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 888, in _execute_text return self.__execute_context(context) File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) sqlalchemy.exc.ProgrammingError: (ProgrammingError) column "chr1" does not exist LINE 1: select * from getsitesnotoverlap_tf (6,149,-1000,chr1,tf) ^ 'select * from getsitesnotoverlap_tf (6,149,-1000,chr1,tf)' {}

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